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View Full Version : Big Y BAM FGC interpretation option and discount for L21



Mikewww
03-06-2015, 06:16 PM
FGC (Full Genomes Corp.) provides interpretations/analyses of Big Y .BAM files for $50 but people in the R-L21 project can get them for only $40 when using our coupon code.

From my perspective, a professional service's value is derived from the people behind the service. This is what I like about FGC's analysis - their consultant, Dr. Greg Magoon. Greg is top-notch, period. He is not just a citizen-scientist. He IS a scientist. He documents and publishes his work. I especially like that he is an R1b specialist as well as a Next Generation Sequencing (NGS) expert. Below are two papers he is an author on:

"Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach"
http://journals.plos.org/plosone/article…

"Generation of high-resolution a priori Y-chromosome phylogenies using 'next-generation” sequencing data'"
http://biorxiv.org/content/early/2013/11/22/000802.1

He is also a key player in ISOGG. I would like to see Greg receive as much L21 data as we can give him. Besides helping us more formally document our tree, I hope our data could be useful in future papers and analysis. We have more NGS tests done than any other subclade so we'd be ideal for a study.

Here is the ordering web site and discount:
https://www.fullgenomes.com/purchases/6/ Coupon code: R1b-L21

This is important. All of this in-depth analysis is of little value if not shared.

In your FGC profile, please share your results with the email ID "l21yresearch@gmail.com". It is a registered account at FGC that I set up for the purpose of more easily sharing .BAM files and interpretation results. Alex Williamson is on board with this and has access to this account so this can help him (which helps us all) better refine the L21 Big Tree as well as proving positioning on more formal trees. I will add a column to the FTDNA kit # to YSEQ ID cross-reference sharing list. We will add FGC kit IDs so we can keep all of this straight in the research and analysis. I maintain this list on the R1b-L21-project yahoo group in conjunction with Mark Jost.

This is just an option that you might consider, but we've already got a number of people engaged in this. The more the merrier!

Petr
03-06-2015, 08:28 PM
Wow, the price is really again $50, I purchased the service on January 6th and on January 30th for $40, so I supposed that the price is lowered to $40 permanently.

Mikewww
03-06-2015, 09:17 PM
Wow, the price is really again $50, I purchased the service on January 6th and on January 30th for $40, so I supposed that the price is lowered to $40 permanently.

Just to be clear. FGC has told me the price is now $50 for this interpretation service, which appears competitive.

L21 project people get a special discount so for them, the price is $40, as long as they use discount coupon code.

rod
03-06-2015, 10:48 PM
How long does it take to get BigY interpretation results?

MitchellSince1893
03-06-2015, 11:22 PM
It varies, but 2 to 4 weeks is in the ball park

rivergirl
03-07-2015, 02:42 AM
I'm not sure how to pass the BAM data to FGC.
I thought there was a new Share link, but I cannot see anything to create that on my FTDNA accounts.
Do I have to download the BAM files and email them to FGC?
I tried this ages ago and it failed.

rod
03-07-2015, 07:00 AM
I have a share link. I'm not sure how long it's good. If it's gone, you may have to request it again.
3967

Mikewww
03-07-2015, 02:49 PM
How long does it take to get BigY interpretation results?
I received mine in about a week.

Petr
03-07-2015, 03:02 PM
How long does it take to get BigY interpretation results?
Ordered on Jan 6th, results received on Jan 9th.
Ordered on Jan 30th, results received on Feb 19th.

Mikewww
03-07-2015, 11:17 PM
We've now got over 40 L21 folks already signed up and sharing their .BAM data and FGC interpretations through the l21yresearch@gmail.com account at FGC. Great start for 24 hours!

rivergirl
04-27-2015, 08:19 AM
Have ordered the BAM interpretation at long last, just waiting on the file link from FTDNA.
83115. T Whelan. CTS1751.
Have your email in the contact section.

Mikewww
04-27-2015, 11:55 AM
Have ordered the BAM interpretation at long last, just waiting on the file link from FTDNA.
83115. T Whelan. CTS1751.
Have your email in the contact section.
When you get your interpretation back from FGC, please hit the "Share" button and enter l21yresearch@gmail.com as the FGC profile to share with. This lets Alex Williamson and James Kane see it too. Alex uses these for diagnostics and tie-breakers in the Big Tree for L21.

rivergirl
05-06-2015, 12:19 AM
When you get your interpretation back from FGC, please hit the "Share" button and enter l21yresearch@gmail.com as the FGC profile to share with. This lets Alex Williamson and James Kane see it too. Alex uses these for diagnostics and tie-breakers in the Big Tree for L21.

Ok Mike, I have the shared the file with l21yresearch@gmail.com
UZ7DA - for Kit 83115, Whelan CTS1751. It might show with my mane instead of Whelan?

How do I access the results myself, all I can see is a Download Bam file link?

Mikewww
05-06-2015, 03:00 AM
Ok Mike, I have the shared the file with l21yresearch@gmail.com
UZ7DA - for Kit 83115, Whelan CTS1751. It might show with my mane instead of Whelan?

How do I access the results myself, all I can see is a Download Bam file link?

Thank you, Rivergirl. On mine, when I log in I can see my haplogroup compare and variant compare files. They take a little while to figure out, but they do have a lot of info in them. Alex Williamson will use the details as well as the .BAM file as needed to do diagnostics and break ties on how the tree should be displayed.

rivergirl
05-13-2015, 08:57 AM
Mike, the Interpretation Results are in for UZ7DA, (Whelan 83115)

Is anyone using the STRs for comparison?

Mikewww
05-13-2015, 11:10 AM
Mike, the Interpretation Results are in for UZ7DA, (Whelan 83115)

Thank you. There is one additional step. Please go into your FGC profile and "Share" your FGC interpretation and analysis with

l21yresearch at gmail dot com

The first letter is an L as in L21.

This allows Alex Williamson to review the interpretation and .BAM file itself so it is a nice mechanism for sharing.

Alex uses these for deep diagnostics and tie breakers in building the Big Tree. He's doing this for free so you want to give him the best details we can.


Is anyone using the STRs for comparison?

I have twice started to pull those STRs in but both times been advised (individual emails so I can't share) that there are concerns about these, particularly STRs called by Yfull. I don't know, but I plan to do this not to replace 111 STRs but as additional information. I don't see how having more data can hurt.

I'm saying that some day you might see an L21 spreadsheet with just people who have 111 STRs, Big Y and FGC interpretations. That would include those extra STRs from the interpretations.

rivergirl
05-13-2015, 03:32 PM
Thanks Mike,

The L21reseach email is already set as sharing the results. (MW Projectadmin)
The kit will probably show up under the name "F James" rather than "Whelan".
The kit number is UZ7DA

I do realise the 111 STRs are not all the same results as reported as FTDNA, (I can see a few differences with my relatives
results) but possibly with the additional yfull STR results, you might find some connections.
As you say, the more info can't hurt.

oneillabu
05-13-2015, 10:14 PM
Thank you. There is one additional step. Please go into your FGC profile and "Share" your FGC interpretation and analysis with

l21yresearch at gmail dot com

This allows Alex Williamson to review the interpretation and .BAM file itself so it is a nice mechanism for sharing.



Just a word of warning, I have an old Windows XP machine with 1GB of RAM and after spending the money to get this done with Fullgenomes I could not download the file and even if I could the only software I could get for interpretation required a 64 bit computer, when I contacted them they recomended that I share the bam file so I shared it out to l21yresearch a long time ago and nothing happened so this whole excercise was a complete waste of money.

lgmayka
05-13-2015, 10:47 PM
Just a word of warning, I have an old Windows XP machine with 1GB of RAM and after spending the money to get this done with Fullgenomes I could not download the file and even if I could the only software I could get for interpretation required a 64 bit computer, when I contacted them they recomended that I share the bam file so I shared it out to l21yresearch a long time ago and nothing happened so this whole excercise was a complete waste of money.
Does FullGenomes offer the option of a BAM file hyperlink, as FTDNA does? If so, you could get YFull's analysis of your BAM file. (Of course, that would be another $49.)

Mikewww
05-13-2015, 11:05 PM
Just a word of warning, I have an old Windows XP machine with 1GB of RAM and after spending the money to get this done with Fullgenomes I could not download the file and even if I could the only software I could get for interpretation required a 64 bit computer, when I contacted them they recomended that I share the bam file so I shared it out to l21yresearch a long time ago and nothing happened so this whole excercise was a complete waste of money.
Oneillabu, if you are talkinbg about the .BAM file you are correct this is a pain to download.... however, there is no need for you to download the BAM file unless you enjoy the pain or love the oodles and oodles of details.

That is the benefit of this process. Request the link from FTDNA if you don't have the link in your Big Y results screen. When the link is there copy and paste it in an email to FGC as they request. They will help guide you.

FGC provides the sharing mechanism. You never have to touch the .BAM file. FGC consultants as well as Alex Williamson can update their trees based on the interpretation. They go directly to the FGC web site to do this.

It is true the benefits to you may not be readily be visible , but you have to go in and look at the interpretation haplogroup and variant compare files which you may not be interested in. If you are not interested in that, the benefits are still there. They become a part of FGC's updated phylogeny (tree) and Alex's updated Big Tree, which both YSEQ and project admins (which means FTDNA) use to update public trees and new fixed SNP panel products.
http://ytree.net/
These folks are using this detailed analysis of Big Y from FGC to identify more stable SNPs and valuable ones that mark branches.

Lgmayka, we have a special profile for L21 people called l21yresearch at gmail dot com that Alex Williamson uses to look at and download the information as needed. This process works well... or at least Alex has never complained about it. He's free, thank God.

MacUalraig
05-14-2015, 09:29 AM
Just a word of warning, I have an old Windows XP machine with 1GB of RAM and after spending the money to get this done with Fullgenomes I could not download the file and even if I could the only software I could get for interpretation required a 64 bit computer, when I contacted them they recomended that I share the bam file so I shared it out to l21yresearch a long time ago and nothing happened so this whole excercise was a complete waste of money.

Did you liaise with your 'local' haplogroup project? Most have at least one person actively analysing raw sequencing data.

Mikewww
05-14-2015, 12:01 PM
... we have a special profile for L21 people called l21yresearch at gmail dot com that Alex Williamson uses to look at and download the information as needed. This process works well....
I should add that for L21 we have a cross-reference ID system so we can merge data from multiple testing and analysis sources.

If anyone would like to make available their FTDNA kit #, FGC kit # (and let us know if this was an interpretation only vs a full NGS test), Yseq ID and Yfull ID -
Please post it here and I'll add you to the list. Researchers like Alex Williamson, Mark Jost and James Kane use this. M222 researches are welcome to use it as well. I use it to merge STRs and multiple SNP results into one file with MDKA info, etc.

oneillabu
05-15-2015, 08:49 PM
Thanks for the advice, I contacted Alex Williamson who sent me the link below with some excellent screenshots

http://www.ytree.net/Instructions.html

Regards

rms2
07-11-2015, 12:18 PM
This morning I ordered the FGC analysis on Mike's advice using the discount code. Thanks, Mike!

Now I'm looking forward to seeing the results.

Mikewww
07-11-2015, 02:12 PM
This morning I ordered the FGC analysis on Mike's advice using the discount code. Thanks, Mike!

Now I'm looking forward to seeing the results.
Thanks to Justin L for giving us the discount for L21 project members.

We have another reason for (a) Big Y folks to FGC interpretations done, and for (b) Big Y and FGC Elite folks to share (blue button) with the administrator profile l21yresearch at gmail.com. Alex W, James K and I have access to that account which means James can include you in his analysis. James K is doing a .BAM file analysis across P312 and is including ancestral calls.

thetick
07-18-2015, 03:31 PM
Thanks to Justin L for giving us the discount for L21 project members.

We have another reason for (a) Big Y folks to FGC interpretations done, and for (b) Big Y and FGC Elite folks to share (blue button) with the administrator profile l21yresearch at gmail.com. Alex W, James K and I have access to that account which means James can include you in his analysis. James K is doing a .BAM file analysis across P312 and is including ancestral calls.

So I'm P312+ DF27+ SRY2627+ CTS4299+. Is the discount available for me or only L21 exclusive club? I'm also on the DF27 and P312 Yahoo projects if that matters?

rms2
07-21-2015, 10:32 AM
First off, I would like to thank Alex Williamson for the fine work he is doing. His Big Tree stuff is pretty amazing. I also want to thank my buddy Dave (jdean) for helping me understand and interpret my Big Y results.

Anyway, I am wondering if there is some kind of simple program available for comparing the novel variants one shares with one individual with those he shares with a second individual to see if there are differences.

JamesKane
07-22-2015, 11:29 PM
The Excel file I'm preparing with all the kits shared in with the account kind of does this, but may not have all the information you are looking for. What you are asking for could be accomplished with auto filters. For instance selecting green colored rows for your kit's column, filtering the order column to the largest value, and the positive column to 2 or 3. Effectively this would show you the variants shared by yourself and the matches around you. You'll also get a fair amount of noise from unstable mutations scattered all around, but these can be eliminated by filtering green on the kits you want to match.

The limitation is the kits included. There are only 158 of the total 234 processed results who have granted permissions as of today. Some of them (like yours) I haven't gotten around to mailing yet.

The sheet will eventually be replaced with more accessible HTML-based grid tables. I need to create some services to provide the data and filtering first.

Mike has something very similar in his discovery sheet. His is based on the VCF/BEDs and includes pretty much all the L21 men. The link is shared with some frequency in the Yahoo L21 group.

rms2
07-23-2015, 12:02 AM
The Excel file I'm preparing with all the kits shared in with the account kind of does this, but may not have all the information you are looking for. What you are asking for could be accomplished with auto filters. For instance selecting green colored rows for your kit's column, filtering the order column to the largest value, and the positive column to 2 or 3. Effectively this would show you the variants shared by yourself and the matches around you. You'll also get a fair amount of noise from unstable mutations scattered all around, but these can be eliminated by filtering green on the kits you want to match.

The limitation is the kits included. There are only 158 of the total 234 processed results who have granted permissions as of today. Some of them (like yours) I haven't gotten around to mailing yet.

The sheet will eventually be replaced with more accessible HTML-based grid tables. I need to create some services to provide the data and filtering first.

Mike has something very similar in his discovery sheet. His is based on the VCF/BEDs and includes pretty much all the L21 men. The link is shared with some frequency in the Yahoo L21 group.

What mailing do you need? I'm willing.

thetick
08-08-2015, 04:13 PM
What mailing do you need? I'm willing.

I think he means https://groups.yahoo.com/neo/groups/R1b-L21-Project/info
I'm a member of R1b-DF-27 Project and R1b-P312-Project. No need to join to see the messages. You will need to join to download/upload files.

JamesKane
08-09-2015, 03:46 PM
Correct, the process is pretty simple. Send an email to my account stating it is okay to analyze and display the Y DNA data in your BAM file. I sent emails to everyone in who has shared with the L21yresearch account early last month. Most have replied and have been added. Those who shared after that email will be asked when I do a second round.

Sometime in the next few months, everyone I have BAMs for will be realigned to human reference b38 instead of hg19/b37. The external support files I needed to do this have been added to the 1000 Genomes project site. The hypothesis is that the more accurate reference genome will clear up some of the ambiguous alignments.

yussef961
09-09-2015, 03:42 PM
the coupon seems to work even if you're j2 great thx

Bart
10-13-2015, 07:33 AM
Purchased today, results to follow, share to follow, thanks Mike.

Not sure how much additional info will come back as think I've already shared BAM with Alex & most people, but anything to help expand the tree. At very least it might expand my current 67 Y-STR's?

Kit: 338578 (DF23>Z2961>ZP75/ZP76>ZP77>ZP92)


Bart

Bart
10-23-2015, 07:42 AM
Purchased today, results to follow, share to follow, thanks Mike.

Not sure how much additional info will come back as think I've already shared BAM with Alex & most people, but anything to help expand the tree. At very least it might expand my current 67 Y-STR's?

Kit: 338578 (DF23>Z2961>ZP75/ZP76>ZP77>ZP92)


Bart

Received back & shared. RHSVB


Bart